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AnnData Single-Cell Data Structure

Teaches Claude how to create, read, concatenate and optimize AnnData objects (.h5ad/.zarr) in the scverse ecosystem.

Data & AnalyticsIntermediate★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

Gives Claude accurate, version-aware knowledge of AnnData, the annotated-matrix format behind Scanpy, scvi-tools and the wider scverse stack.

  • Explains X, obs, var, layers, obsm/varm, obsp/varp, uns, raw
  • I/O for h5ad, zarr, CSV, MTX, Loom, plus compression and backed mode
  • ad.concat() patterns: inner/outer joins, merge strategies, batch labels, lazy AnnCollection
  • Subsetting, views vs copies, sparse and categorical conversions for memory efficiency
  • Flags deprecated APIs and points to the modern anndata.io namespace

Who it's for

  • scRNA-seq researchers pairing AnnData with scanpy/scvi-tools/muon
  • Data engineers streaming multi-gigabyte h5ad files without blowing up RAM
  • Bioinformaticians merging many experimental batches into one object

Examples

  1. "Open this 100GB h5ad in backed mode, keep cells with quality_score > 0.8, and process in 1000-row chunks."
  2. "Concatenate batch1-3 with an inner join, add batch labels, then run combat correction and UMAP."
  3. "My AnnData object is huge — convert X to CSR, cast strings to categoricals, and rewrite with gzip."

· · · Install guide · · ·

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/anndata folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/anndata/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills && mkdir -p ~/.claude/skills && cp -r /tmp/scientific-agent-skills/skills/anndata ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal.
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills
  3. Create the skills folder: mkdir -p ~/.claude/skills
  4. Copy just this skill: cp -r /tmp/scientific-agent-skills/skills/anndata ~/.claude/skills/
  5. Verify the bundled references/ docs came along: ls ~/.claude/skills/anndata
  6. Install the library (Python 3.11+ required): uv pip install "anndata==0.12.16"
  7. Restart Claude Code and try a prompt like "Load data.h5ad and subset to T cells" to trigger the skill.
View source on GitHub ↗License: MIT